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- PDB-3vk6: Crystal structure of a phosphotyrosine binding domain -

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Basic information

Entry
Database: PDB / ID: 3vk6
TitleCrystal structure of a phosphotyrosine binding domain
ComponentsE3 ubiquitin-protein ligase Hakai
KeywordsLIGASE / HYB / Phosphotyrosine Binding Domain
Function / homology
Function and homology information


RNA N6-methyladenosine methyltransferase complex / Antigen processing: Ubiquitination & Proteasome degradation / : / negative regulation of cell adhesion / positive regulation of endocytosis / regulation of cell adhesion / RING-type E3 ubiquitin transferase / cell-cell adhesion / ubiquitin protein ligase activity / protein ubiquitination ...RNA N6-methyladenosine methyltransferase complex / Antigen processing: Ubiquitination & Proteasome degradation / : / negative regulation of cell adhesion / positive regulation of endocytosis / regulation of cell adhesion / RING-type E3 ubiquitin transferase / cell-cell adhesion / ubiquitin protein ligase activity / protein ubiquitination / positive regulation of cell migration / nuclear speck / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Helix Hairpins - #2210 / HAKAI-like, RING finger, HC subclass / E3 ubiquitin-protein ligase HAKAI/CBLL2 / Hakai, C2H2 zinc finger domain / C2H2 Hakai zinc finger domain / Helix Hairpins / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...Helix Hairpins - #2210 / HAKAI-like, RING finger, HC subclass / E3 ubiquitin-protein ligase HAKAI/CBLL2 / Hakai, C2H2 zinc finger domain / C2H2 Hakai zinc finger domain / Helix Hairpins / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Helix non-globular / Zinc finger RING-type profile. / Zinc finger, RING-type / Special / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Hakai
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSivaraman, J. / Mukherjee, M.
CitationJournal: Embo J. / Year: 2012
Title: Structure of a novel phosphotyrosine-binding domain in Hakai that targets E-cadherin
Authors: Mukherjee, M. / Chow, S.Y. / Yusoff, P. / Seetharaman, J. / Ng, C. / Sinniah, S. / Koh, X.W. / Asgar, N.F. / Li, D. / Yim, D. / Jackson, R.A. / Yew, J. / Qian, J. / Iyu, A. / Lim, Y.P. / ...Authors: Mukherjee, M. / Chow, S.Y. / Yusoff, P. / Seetharaman, J. / Ng, C. / Sinniah, S. / Koh, X.W. / Asgar, N.F. / Li, D. / Yim, D. / Jackson, R.A. / Yew, J. / Qian, J. / Iyu, A. / Lim, Y.P. / Zhou, X. / Sze, S.K. / Guy, G.R. / Sivaraman, J.
History
DepositionNov 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Hakai
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7514
Polymers11,5551
Non-polymers1963
Water1,26170
1
A: E3 ubiquitin-protein ligase Hakai
hetero molecules

A: E3 ubiquitin-protein ligase Hakai
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5028
Polymers23,1092
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area3680 Å2
ΔGint-116 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.657, 64.657, 121.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-138-

HOH

21A-163-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase Hakai / Casitas B-lineage lymphoma-transforming sequence-like protein 1 / E-cadherin binding protein E7 / c- ...Casitas B-lineage lymphoma-transforming sequence-like protein 1 / E-cadherin binding protein E7 / c-Cbl-like protein 1


Mass: 11554.673 Da / Num. of mol.: 1
Fragment: Phosphotyrosine Binding Domain, UNP residues 106-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbll1, Hakai / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9JIY2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 % / Description: SF file contains friedel pairs.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200mM Li2SO4, 100mM Tris, 20% PEG 5000 MME, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 22371 / Num. obs: 21480 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 22.8 % / Biso Wilson estimate: 31.95 Å2 / Rsym value: 0.052 / Net I/σ(I): 21.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 22.8 % / Num. unique all: 21480 / Rsym value: 0.052 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→25.228 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8413 / SU ML: 0.23 / σ(F): 0.24 / Phase error: 22.6 / Stereochemistry target values: ML / Details: SF File contains friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 2153 10.02 %RANDOM
Rwork0.2192 ---
all0.2277 ---
obs0.2216 21478 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.07 Å2 / ksol: 0.419 e/Å3
Displacement parametersBiso max: 67.32 Å2 / Biso mean: 38.936 Å2 / Biso min: 24.08 Å2
Baniso -1Baniso -2Baniso -3
1-3.4846 Å20 Å2-0 Å2
2--3.4846 Å20 Å2
3----6.9693 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 3 70 828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008771
X-RAY DIFFRACTIONf_angle_d1.1721031
X-RAY DIFFRACTIONf_dihedral_angle_d13.796297
X-RAY DIFFRACTIONf_chiral_restr0.081108
X-RAY DIFFRACTIONf_plane_restr0.006133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8971-1.96490.25542050.2445180389
1.9649-2.04360.26452060.2372187493
2.0436-2.13650.242160.2249192195
2.1365-2.24910.25592200.2156193296
2.2491-2.38990.21432130.2058194796
2.3899-2.57430.23492120.2173193496
2.5743-2.8330.24982130.2294195497
2.833-3.24220.27242260.2246199198
3.2422-4.08210.22122250.199199999
4.0821-25.23050.23512170.2219197097

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